forked from lijiext/lammps
240 lines
7.7 KiB
HTML
240 lines
7.7 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
|
|
<HTML>
|
|
<HEAD>
|
|
<META NAME="Generator" CONTENT="Cosmo Create 1.0.3">
|
|
</HEAD>
|
|
<BODY>
|
|
<H2>
|
|
LAMMPS Data Format</H2>
|
|
<P>
|
|
<A HREF="README.html">Return</A> to top-level of LAMMPS documentation</P>
|
|
<P>
|
|
This file describes the format of the data file read into LAMMPS with
|
|
the "read data" command. The data file contains basic
|
|
information about the size of the problem to be run, the initial atomic
|
|
coordinates, molecular topology, and (optionally) force-field
|
|
coefficients. It will be easiest to understand this file if you read it
|
|
while looking at a sample data file from the examples.</P>
|
|
<P>
|
|
This page has 2 sections:</P>
|
|
<UL>
|
|
<LI>
|
|
<A HREF="#_cch3_930958962">Rules for formatting the Data File</A>
|
|
<LI>
|
|
<A HREF="#_cch3_930958969">Sample file with Annotations</A>
|
|
</UL>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_930958962">Rules for formatting the Data File: </A></H3>
|
|
<P>
|
|
Blank lines are important. After the header section, new entries are
|
|
separated by blank lines. </P>
|
|
<P>
|
|
Indentation and space between words/numbers on one line is not
|
|
important except that entry keywords (e.g. Masses, Bond Coeffs) must be
|
|
left-justified and capitalized as shown. </P>
|
|
<P>
|
|
The header section (thru box bounds) must appear first in the file, the
|
|
remaining entries (Masses, various Coeffs, Atoms, Bonds, etc) can come
|
|
in any order. </P>
|
|
<P>
|
|
These entries must be in the file: header section, Masses, Atoms. </P>
|
|
<P>
|
|
These entries must be in the file if there are a non-zero number of
|
|
them: Bonds, Angles, Dihedrals, Impropers, Bond Coeffs, Angle Coeffs,
|
|
Dihedral Coeffs, Improper Coeffs. Cross-term coefficients for a
|
|
particular kind of interaction (e.g. BondAngle Coeffs for bonds) must
|
|
appear if class II force fields have been turned on in the input
|
|
command file via a "style" command. </P>
|
|
<P>
|
|
The Nonbond Coeffs entry contains one line for each atom type. These
|
|
are the coefficients for an interaction between 2 atoms of the same
|
|
type. The cross-type coeffs are computed by the appropriate class I or
|
|
class II mixing rules, or can be specified explicitly using the
|
|
"nonbond coeff" command in the input command script. See the <A
|
|
HREF="force_fields.html">force_fields</A> page for more information. </P>
|
|
<P>
|
|
The Nonbond Coeffs and Bond Coeffs entries are optional since they can
|
|
be specified from the input command script. This is not true if bond
|
|
style is set to class II since those coeffs can only be specified in
|
|
this data file. </P>
|
|
<P>
|
|
In the Atoms entry, the atoms can be in any order so long as there are
|
|
N entries. The 1st number on the line is the atom-tag (number from 1 to
|
|
N) which is used to identify the atom throughout the simulation. The
|
|
molecule-tag is a second identifier which is attached to the atom; it
|
|
can be 0, or a counter for the molecule the atom is part of, or any
|
|
other number you wish. The q value is the charge of the atom in
|
|
electron units (e.g. +1 for a proton). The xyz values are the initial
|
|
position of the atom. For 2-d simulations specify z as 0.0.</P>
|
|
<P>
|
|
The final 3 nx,ny,nz values on a line of the Atoms entry are optional.
|
|
LAMMPS only reads them if the "true flag" command is
|
|
specified in the input command script. Otherwise they are initialized
|
|
to 0 by LAMMPS. Their meaning, for each dimension, is that
|
|
"n" box-lengths are added to xyz to get the atom's
|
|
"true" un-remapped position. This can be useful in pre- or
|
|
post-processing to enable the unwrapping of long-chained molecules
|
|
which wrap thru the periodic box one or more times. The value of
|
|
"n" can be positive, negative, or zero. For 2-d simulations
|
|
specify nz as 0. </P>
|
|
<P>
|
|
For simulations with periodic boundary conditions, xyz are remapped
|
|
into the periodic box (from as far away as needed), so the initial
|
|
coordinates need not be inside the box. The nx,ny,nz values (as read in
|
|
or as set to zero by LAMMPS) are appropriately adjusted by this
|
|
remapping. </P>
|
|
<P>
|
|
The number of coefficients specified on each line of coefficient
|
|
entries (Nonbond Coeffs, Bond Coeffs, etc) depends on the
|
|
"style" of interaction. This is specified in the input
|
|
command script, unless the default is used. See the <A
|
|
HREF="input_commands.html">input_commands</A> page for a description
|
|
of the various style options. The <A HREF="input_commands.html">input_commands</A>
|
|
and <A HREF="force_fields.html">force_fields</A> pages explain the
|
|
meaning and valid ranges for each of the coefficients. </P>
|
|
<HR>
|
|
<H3>
|
|
<A NAME="_cch3_930958969">Sample file with Annotations</A></H3>
|
|
<P>
|
|
Here is a sample file with annotations in parenthesis and lengthy
|
|
sections replaced by dots (...). Note that the blank lines are
|
|
important in this example.</P>
|
|
<PRE>
|
|
|
|
LAMMPS Description (1st line of file)
|
|
|
|
100 atoms (this must be the 3rd line, 1st 2 lines are ignored)
|
|
95 bonds (# of bonds to be simulated)
|
|
50 angles (include these lines even if number = 0)
|
|
30 dihedrals
|
|
20 impropers
|
|
|
|
5 atom types (# of nonbond atom types)
|
|
10 bond types (# of bond types = sets of bond coefficients)
|
|
18 angle types
|
|
20 dihedral types (do not include a bond,angle,dihedral,improper type
|
|
2 improper types line if number of bonds,angles,etc is 0)
|
|
|
|
-0.5 0.5 xlo xhi (for periodic systems this is box size,
|
|
-0.5 0.5 ylo yhi for non-periodic it is min/max extent of atoms)
|
|
-0.5 0.5 zlo zhi (do not include this line for 2-d simulations)
|
|
|
|
Masses
|
|
|
|
1 mass
|
|
...
|
|
N mass (N = # of atom types)
|
|
|
|
Nonbond Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of atom types)
|
|
|
|
Bond Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of bond types)
|
|
|
|
Angle Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of angle types)
|
|
|
|
Dihedral Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of dihedral types)
|
|
|
|
Improper Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of improper types)
|
|
|
|
BondBond Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of angle types)
|
|
|
|
BondAngle Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of angle types)
|
|
|
|
MiddleBondTorsion Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of dihedral types)
|
|
|
|
EndBondTorsion Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of dihedral types)
|
|
|
|
AngleTorsion Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of dihedral types)
|
|
|
|
AngleAngleTorsion Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of dihedral types)
|
|
|
|
BondBond13 Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of dihedral types)
|
|
|
|
AngleAngle Coeffs
|
|
|
|
1 coeff1 coeff2 ...
|
|
...
|
|
N coeff1 coeff2 ... (N = # of improper types)
|
|
|
|
Atoms
|
|
|
|
1 molecule-tag atom-type q x y z nx ny nz (nx,ny,nz are optional -
|
|
... see "true flag" input command)
|
|
...
|
|
N molecule-tag atom-type q x y z nx ny nz (N = # of atoms)
|
|
|
|
Bonds
|
|
|
|
1 bond-type atom-1 atom-2
|
|
...
|
|
N bond-type atom-1 atom-2 (N = # of bonds)
|
|
|
|
Angles
|
|
|
|
1 angle-type atom-1 atom-2 atom-3 (atom-2 is the center atom in angle)
|
|
...
|
|
N angle-type atom-1 atom-2 atom-3 (N = # of angles)
|
|
|
|
Dihedrals
|
|
|
|
1 dihedral-type atom-1 atom-2 atom-3 atom-4 (atoms 2-3 form central bond)
|
|
...
|
|
N dihedral-type atom-1 atom-2 atom-3 atom-4 (N = # of dihedrals)
|
|
|
|
Impropers
|
|
|
|
1 improper-type atom-1 atom-2 atom-3 atom-4 (atom-1 is central atom)
|
|
...
|
|
N improper-type atom-1 atom-2 atom-3 atom-4 (N = # of impropers)
|
|
</PRE>
|
|
</BODY>
|
|
</HTML>
|